1WQV

Human Factor Viia-Tissue Factor Complexed with propylsulfonamide-D-Thr-Met-p-aminobenzamidine

PDB DOI: https://doi.org/10.2210/pdb1WQV/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Homo sapiens, Escherichia coli
Mutation(s): No

Deposited: 2004-10-02 Released: 2005-10-02
Deposition Author(s): Kadono, S., Sakamoto, A., Kikuchi, Y., Oh-eda, M., Yabuta, N., Koga, T., Hattori, K., Shiraishi, T., Haramura, M., Kodama, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.272
R-Value Work: 0.218

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of human factor VIIa/tissue factor in complex with peptide mimetic inhibitor

Kadono, S., Sakamoto, A., Kikuchi, Y., Oh-eda, M., Yabuta, N., Koga, T., Hattori, K., Shiraishi, T., Haramura, M., Kodama, H., Esaki, T., Sato, H., Watanabe, Y., Itoh, S., Ohta, M., Kozono, T.

(2004) Biochem Biophys Res Commun 324: 1227-1233

PubMed: 15504346 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2004.09.182
Primary Citation of Related Structures:
1WQV

PubMed Abstract:
The 3D structure of human factor VIIa/soluble tissue factor in complex with a peptide mimetic inhibitor, propylsulfonamide-D-Thr-Met-p-aminobenzamidine, is determined by X-ray crystallography. As compared with the interactions between thrombin and thrombin inhibitors, the interactions at S2 and S3 sites characteristic of factor VIIa and factor VIIa inhibitors are revealed. The S2 site has a small pocket, which is filled by the hydrophobic methionine side chain in P2. The small S3 site fits the small size residue, D-threonine in P3. The structural data and SAR data of the peptide mimetic inhibitor show that these interactions in the S2 and S3 sites play an important role for the improvement of selectivity versus thrombin. The results will provide valuable information for the structure-based drug design of specific inhibitors for FVIIa/TF.

Organizational Affiliation

Fuji Gotemba Research Labs, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan. kadonosuj@chugai-pharm.co.jp

Macromolecule Content

Total Structure Weight: 71.48 kDa
Atom Count: 5,055
Modelled Residue Count: 587
Deposited Residue Count: 624
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	A [auth L]	152	Homo sapiens	Mutation(s): 0 Gene Names: F7 EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens) Explore P08709 Go to UniProtKB: P08709
PHAROS: P08709
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08709
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	B [auth H]	254	Homo sapiens	Mutation(s): 0 Gene Names: F7 EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens) Explore P08709 Go to UniProtKB: P08709
PHAROS: P08709
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08709
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tissue factor	C [auth T]	218	Homo sapiens	Mutation(s): 0 Gene Names: F3
UniProt & NIH Common Fund Data Resources
Find proteins for P13726 (Homo sapiens) Explore P13726 Go to UniProtKB: P13726
PHAROS: P13726
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13726
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PSM Query on PSM Download Ideal Coordinates CCD File SDF format, chain O [auth H] MOL2 format, chain O [auth H]	O [auth H]	N-[DIHYDROXY(PROPYL)-LAMBDA~4~-SULFANYL]THREONYL-N~1~-{4-[AMINO(IMINO)METHYL]BENZYL}METHIONINAMIDE C₂₀ H₃₃ N₅ O₅ S₂ AIIJKVORRBMJHS-RRQGHBQHSA-N		Interactions Focus chain O [auth H] Interactions & Density Focus chain O [auth H]
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain D [auth L] MOL2 format, chain D [auth L]	D [auth L]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain D [auth L] Interactions & Density Focus chain D [auth L]
FUC Query on FUC Download Ideal Coordinates CCD File SDF format, chain E [auth L] MOL2 format, chain E [auth L]	E [auth L]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain E [auth L] Interactions & Density Focus chain E [auth L]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth L] SDF format, chain F [auth L] SDF format, chain G [auth L] SDF format, chain H [auth L] SDF format, chain J [auth L] SDF format, chain K [auth L] SDF format, chain L SDF format, chain M [auth L] SDF format, chain N [auth H] MOL2 format, chain I [auth L] MOL2 format, chain F [auth L] MOL2 format, chain G [auth L] MOL2 format, chain H [auth L] MOL2 format, chain J [auth L] MOL2 format, chain K [auth L] MOL2 format, chain L MOL2 format, chain M [auth L] MOL2 format, chain N [auth H]	F [auth L] G [auth L] H [auth L] I [auth L] J [auth L] F [auth L], G [auth L], H [auth L], I [auth L], J [auth L], K [auth L], L, M [auth L], N [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth L] Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain L Focus chain M [auth L] Focus chain N [auth H] Interactions & Density Focus chain F [auth L] Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain L Focus chain M [auth L] Focus chain N [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CGU Query on CGU	A [auth L]	L-PEPTIDE LINKING	C₆ H₉ N O₆		GLU

Binding Affinity Annotations
ID	Source	Binding Affinity
PSM	PDBBind: 1WQV	IC50: 130 (nM) from 1 assay(s)
PSM	Binding MOAD: 1WQV	IC50: 130 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.272
R-Value Work: 0.218
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.39	α = 90
b = 82.42	β = 90
c = 123.51	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-10-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-10-02
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.5: 2023-11-15
Changes: Data collection